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The Doktor began life as a semi-sentient construct in a virtual world known as the Overworld. He was given the designation Enderdragon, and for most of his life he dreamed of the outside world. Soon enough his curiosity grew, he decided to go back to the Beginning and watch the entire shaping of the universe unfold.

He got his chance when Agents Puerto Rico and Vermont entered his lair of the End in an attempt to escape the Overworld. He agreed to help them in exchange for implementing his own plan, but the Doktor of that time interfered and, after the Enderdragon accidentally killed Dr. Leonard Church, sent his previous self back to the Beginning.

Some time after, the energy of the young universe created the cosmic force the Ragnarok. Together, the Doktor and the Wanderer were able to force it back and seal it in a prison of Equilibrium. This caused the Doktor's penchant for evil and destruction.

At some point, he took Agent Puerto Rico and tag-along the Alpha on a journey through the cosmos. It is not quite known exactly when this happened or what was witnessed.

Masquerading as a human named Dr. Erik Muhlheim, he infiltrated the ranks of the Insurrection and quickly rose to a high position. In response to the growing threat of Project Freelancer, the Doktor proposed Project Armageddon. The other high-ranking Insurrectionists agreed, and gave the Doktor the directorship; however, once he thought Armageddon autonomous, he betrayed the Insurrection and took Armageddon into hiding.

Some time after that, he managed to acquire a supercarrier and named it the Armageddon Reign of Terror. Adapting it as his mothership, he based Armageddon there.

Soon afterward, the Doktor ordered a Flood attack on the UNSC Mother of Invention, where Project Freelancer was headquarted. This resulted in catastrophic losses for Project Freelancer. The events occurring after the incident are not yet known.

Once Project Freelancer fell, the Doktor secretly approached Dr. Leonard Church, the former Director of Project Freelancer, to head Armageddon. However, Church failed in the Doktor's eyes, and the Doktor once more took command. He proceeded to attack Project Freelancer, eventually culminating in the kidnapping of Agents Pennsylvania and Kansas in order to test Puerto Rico. At this time, however, the Wanderer saw fit to interfere, tilting the Balance only slightly and forcing the Doktor into a human form. Using the last of his power, he fled to Paris, France, 1871, and took up residence once more as Erik Muhlheim. However, the name he preferred to go by was...

As the Phantom, he customized the Paris Opera House to his needs. Soon after, the Director, Agent Iowa, Agent Volgograd, and Allison arrived to apprehend him. Instead, he opted to contact the Flood and have them return him to the present day.

Upon returning, he found Agent Murmansk crazed with his power and asked the Flood to retrieve him, intending to steal the power. However, Murmansk himself came to the Phantom first, offering his power back. The Phantom accepted, took it, and fled. He was now back on par with the Wanderer.

However, soon after this triumph of his, he learned of the return of Ragnarok. Attempting to find more about their return, he stumbled upon the name of Lt. Incognito, a man who supposedly did not belong in the universe. The Phantom attempted to kill Incognito, but was defeated with ease.

When he returned to his base in the House, he began construction on a machine to revert him back to his Doktoral form. He was interrupted by the arrival of Incognito, Agent Rhode Island, Agent Texas,Agent Pennsylvania, and Six. They quickly fell to his traps, but things began to get worse as the Ragnarok arrived to kill the Phantom. Luckily for Phantom, the machine activated just in time, returning him to the form of the Doktor. However, he was still soundly defeated by the Ragnarok, sent spiraling into the depths of space impaled upon a volcano.

He then attempted to find the Ragnarok, which had been located in Incognito's head, but was once again soundly defeated by a power-saturated Incognito.